- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.94 Å
- Oligo State
- homo-pentamer
- Ligands
- 5 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)
- 18 x PO4: PHOSPHATE ION(Non-functional Binders)
PO4.2: 8 residues within 4Å:- Chain A: T.112, Y.113, W.148, W.149, F.189
- Chain C: R.206
- Ligands: HEM.1, PO4.24
Ligand excluded by PLIPPO4.3: 4 residues within 4Å:- Chain A: K.143, R.218, R.219
- Chain C: H.222
Ligand excluded by PLIPPO4.4: 4 residues within 4Å:- Chain A: H.222
- Chain E: K.143, R.218, R.219
Ligand excluded by PLIPPO4.5: 5 residues within 4Å:- Chain A: R.197, L.198, E.199, D.200
- Chain E: Y.16
Ligand excluded by PLIPPO4.6: 6 residues within 4Å:- Chain A: H.202, R.206
- Chain E: K.109, H.180, F.189
- Ligands: PO4.38
Ligand excluded by PLIPPO4.12: 4 residues within 4Å:- Chain B: K.143, R.218, R.219
- Chain D: H.222
Ligand excluded by PLIPPO4.13: 4 residues within 4Å:- Chain B: R.197, L.198, E.199
- Chain C: Y.16
Ligand excluded by PLIPPO4.14: 6 residues within 4Å:- Chain B: H.202, R.206
- Chain C: K.109, H.180, F.189
- Ligands: PO4.23
Ligand excluded by PLIPPO4.15: 9 residues within 4Å:- Chain B: T.112, Y.113, W.148, W.149, R.156, F.189
- Chain D: R.206
- Ligands: HEM.11, PO4.30
Ligand excluded by PLIPPO4.22: 4 residues within 4Å:- Chain B: H.222
- Chain C: K.143, R.218, R.219
Ligand excluded by PLIPPO4.23: 9 residues within 4Å:- Chain B: R.206
- Chain C: T.112, Y.113, W.148, W.149, R.156, F.189
- Ligands: PO4.14, HEM.21
Ligand excluded by PLIPPO4.24: 6 residues within 4Å:- Chain A: K.109, H.180, F.189
- Chain C: H.202, R.206
- Ligands: PO4.2
Ligand excluded by PLIPPO4.30: 6 residues within 4Å:- Chain B: K.109, H.180, F.189
- Chain D: H.202, R.206
- Ligands: PO4.15
Ligand excluded by PLIPPO4.31: 4 residues within 4Å:- Chain D: K.143, R.218, R.219
- Chain E: H.222
Ligand excluded by PLIPPO4.32: 8 residues within 4Å:- Chain D: T.112, Y.113, W.148, W.149, F.189
- Chain E: R.206
- Ligands: HEM.29, PO4.33
Ligand excluded by PLIPPO4.33: 6 residues within 4Å:- Chain D: K.109, H.180, F.189
- Chain E: H.202, R.206
- Ligands: PO4.32
Ligand excluded by PLIPPO4.38: 8 residues within 4Å:- Chain A: R.206
- Chain E: T.112, Y.113, W.148, W.149, F.189
- Ligands: PO4.6, HEM.37
Ligand excluded by PLIPPO4.39: 4 residues within 4Å:- Chain D: Y.16
- Chain E: R.197, L.198, E.199
Ligand excluded by PLIP- 5 x CYN: CYANIDE ION(Non-covalent)(Non-functional Binders)
CYN.7: 3 residues within 4Å:- Chain A: L.178
- Ligands: HEM.1, GOL.8
No protein-ligand interaction detected (PLIP)CYN.16: 3 residues within 4Å:- Chain B: L.178
- Ligands: HEM.11, GOL.17
No protein-ligand interaction detected (PLIP)CYN.25: 3 residues within 4Å:- Chain C: L.178
- Ligands: HEM.21, GOL.26
No protein-ligand interaction detected (PLIP)CYN.34: 2 residues within 4Å:- Ligands: HEM.29, GOL.35
No protein-ligand interaction detected (PLIP)CYN.40: 2 residues within 4Å:- Ligands: HEM.37, GOL.41
No protein-ligand interaction detected (PLIP)- 13 x GOL: GLYCEROL(Non-functional Binders)
GOL.8: 4 residues within 4Å:- Chain A: R.176, L.178
- Ligands: HEM.1, CYN.7
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:R.176
- Water bridges: A:L.178, A:L.178
GOL.9: 3 residues within 4Å:- Chain A: Q.49, W.50, K.53
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:K.53
- Water bridges: A:Q.49, A:Q.49, A:W.50
GOL.10: 4 residues within 4Å:- Chain A: K.44, P.231, L.232, D.233
6 PLIP interactions:6 interactions with chain A- Hydrogen bonds: A:L.232, A:D.233, A:D.233
- Water bridges: A:K.44, A:V.56, A:S.230
GOL.17: 5 residues within 4Å:- Chain B: P.111, R.176, L.178
- Ligands: HEM.11, CYN.16
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:R.176
GOL.18: 10 residues within 4Å:- Chain B: G.129, E.130, P.135, K.172, T.173, K.175, E.194, T.195, E.196, R.197
6 PLIP interactions:6 interactions with chain B- Hydrogen bonds: B:E.130, B:K.172, B:K.175, B:E.194, B:E.196, B:R.197
GOL.19: 5 residues within 4Å:- Chain B: S.120, M.121, E.124, Q.165, L.168
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:E.124, B:Q.165
- Water bridges: B:S.120
GOL.20: 4 residues within 4Å:- Chain B: H.222, P.223
- Chain C: D.186, R.219
5 PLIP interactions:3 interactions with chain C, 2 interactions with chain B- Hydrogen bonds: C:D.186, C:R.219, B:H.222, B:H.222
- Water bridges: C:D.186
GOL.26: 5 residues within 4Å:- Chain C: P.111, R.176
- Ligands: HEM.21, CYN.25, GOL.28
3 PLIP interactions:3 interactions with chain C- Hydrogen bonds: C:R.176, C:R.176
- Water bridges: C:L.178
GOL.27: 4 residues within 4Å:- Chain A: D.186, R.219
- Chain C: H.222, P.223
3 PLIP interactions:2 interactions with chain A, 1 interactions with chain C- Hydrogen bonds: A:D.186, A:R.219, C:H.222
GOL.28: 8 residues within 4Å:- Chain C: S.108, K.109, K.110, P.111, L.178, H.180
- Ligands: HEM.21, GOL.26
6 PLIP interactions:6 interactions with chain C- Hydrogen bonds: C:K.109, C:L.178
- Water bridges: C:K.110, C:T.112, C:H.180, C:H.180
GOL.35: 5 residues within 4Å:- Chain D: P.111, R.176, L.178
- Ligands: HEM.29, CYN.34
2 PLIP interactions:2 interactions with chain D- Hydrogen bonds: D:R.176, D:L.178
GOL.36: 8 residues within 4Å:- Chain B: Y.16, T.78, L.79
- Chain D: Y.136, E.196, R.197, L.198, E.199
6 PLIP interactions:5 interactions with chain D, 1 interactions with chain B- Hydrogen bonds: D:Y.136, D:L.198, D:E.199, B:L.79
- Water bridges: D:R.197, D:D.200
GOL.41: 6 residues within 4Å:- Chain E: P.111, V.114, R.176, L.178
- Ligands: HEM.37, CYN.40
2 PLIP interactions:2 interactions with chain E- Hydrogen bonds: E:R.176
- Water bridges: E:L.178
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Kostan, J. et al., Structural and functional characterisation of the chlorite dismutase from the nitrite-oxidizing bacterium "Candidatus Nitrospira defluvii": Identification of a catalytically important amino acid residue. J.Struct.Biol. (2010)
- Release Date
- 2010-07-28
- Peptides
- Chlorite dismutase: ABCDE
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
DE
E
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.94 Å
- Oligo State
- homo-pentamer
- Ligands
- 5 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)
- 18 x PO4: PHOSPHATE ION(Non-functional Binders)
- 5 x CYN: CYANIDE ION(Non-covalent)(Non-functional Binders)
- 13 x GOL: GLYCEROL(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Kostan, J. et al., Structural and functional characterisation of the chlorite dismutase from the nitrite-oxidizing bacterium "Candidatus Nitrospira defluvii": Identification of a catalytically important amino acid residue. J.Struct.Biol. (2010)
- Release Date
- 2010-07-28
- Peptides
- Chlorite dismutase: ABCDE
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
DE
E